[gmx-users] Umbrella sampling with temperature and pressure coupling method problem

Justin A. Lemkul jalemkul at vt.edu
Tue Oct 19 15:30:47 CEST 2010

chris.neale at utoronto.ca wrote:
> Use Langevin dynamics (the sd integrator) to control the temperature. 
> You are sure to get the correct ensemble that way and if you are doing 
> US then you can not extract dynamics anyway.
> Hopefully somebody else can address the pressure coupling for you, but 
> probably you need to provide more information to get a useful answer there.

The Berendsen barostat suffers from the same limitations as the thermostat - the 
pressure distribution does not produce a true NPT ensemble.


> -- original message --
> Dear all,
>     I want to use umbrella sampling to calculate the PMF of the
> conformational transition of a protein. What temperature coupling method 
> and
> pressure coupling method should I use? Berendsen temperature coupling or
> Nose-Hoover temperature coupling? Or each one is OK?


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list